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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS, POPULATION BIOLOGY, AND HOST-PARASITE INTERACTIONS OF CEREAL RUST FUNGI AND THEIR DISEASES

Location: Cereal Disease Laboratory

2011 Annual Report


1a.Objectives (from AD-416)
New funds will be used to expand the current research objectives for this ARS project to prepare for the possible appearance of Ug99 in North America. Those objectives are:

Objective 1: Monitor and characterize races of cereal rust pathogens, particularly the new East African strain, Ug99. This includes the sub-objective of characterizing races of cereal stem rust, particularly Ug99 and related mutants, which represent a threat to the production of wheat, oat, and barley cultivars in the United States.

Objective 2: Identify features essential for cereal rust pathogensis including sub-objectives of characterizing the genome of Puccinia graminis (stem rust). Research for this objective will be expanded to characterize the Ug99 genome sequence and to develop detection methods for the new Eastern African stem rust mutants.

Objective 3: Identify resistance genes and develop effective strategies for deploying host-resistance genes to control cereal rust diseases. Research for this objective will be expanded to identify new sources of Ug99 resistance and to accelerate the development of Ug99-resistant wheat and barley varieties adapted for U.S. production.


1b.Approach (from AD-416)
Cereal rust pathogens continuously evolve to overcome existing host resistance genes in wheat, barley, and oats. Cereal germplasm with durable rust resistance, and other control strategies are needed to minimize yield losses due to cereal rusts. Variation in cereal rust populations will be analyzed by assessing virulence polymorphism to important rust resistance genes and by using molecular polymorphism to determine the relatedness and relationships between these populations. Migration patterns of cereal rust populations will be established using virulence and molecular markers. Virulence shifts in cereal rust populations in major cereal-producing areas of the U.S. in relation to use of rust resistance genes will be analyzed. Cereal germplasm with rust resistance will be evaluated in seedling plant tests and in adult plant field tests. Advanced germplasm lines with combinations of rust resistance genes will be selected. Cereal germplasm with durable resistance will be genetically analyzed to determine the identity and expression of the rust resistance genes. A genetic map of P. graminis will be constructed using AFLPs, SSRs, and SNPs. Physical maps of regions with avirulence genes will be developed using BAC and cosmid libraries. Genetic determinants of early infection processes in cereal rusts will be characterized. Crosses will be made with other cereal rust fungi to determine the genetics of avirulence/virulence to important rust resistance genes.


3.Progress Report
In 2011, monitoring for leaf rust (wheat and barley), stem rust (wheat, barley, oat) and crown rust (oat) in the United States was conducted. Updates were provided to agricultural professionals and growers. Race identification was completed for 2010 collections. Forty-one races of wheat leaf rust pathogen were described with three common races accounting for two-thirds of the samples. Virulence to the leaf rust resistance gene Lr21 was detected for the first time in North America. The predominantly grown hard red and soft red winter wheat cultivars are susceptible to these common races of leaf rust pathogen, which results in regular yield losses in wheat. Two races of Puccinia graminis f. sp. tritici were identified from 60 wheat stem rust samples collected from the United States eastern of the Rocky Mountains. The majority of the samples (59/60) were race QFCSC. Thirty-one races of P. graminis f. sp. tritici were identified from 13 stem rust samples collected from eastern Washington and western Idaho. Diverse virulence types indicated an active sexual cycle is present in the region. Crown rust severity was generally light throughout much of the United States in 2010. A total of 142 isolates of P. coronata, consisting of 95 races, were collected in the 2010 survey. Virulence to Pc91 and Pc94 was low, indicating that these genes are still effective. A project for characterization of barley leaf rust pathogens in the United States was initiated.

Potential sources of effective, new crown rust resistance genes were found among 338 accessions of tetraploid and diploid wild Avena species from Morocco. A new statistical approach to identifying potential sources of partial resistance to oat crown rust was tested using data from the Saint Paul oat/buckthorn crown rust nursery and appears promising. Mapping of partial resistance to crown rust in the PI260616/Otana RI population has revealed new resistance QTL.

Genetic analysis was conducted to determine the nature of resistance to wheat leaf rust pathogen in two wheat lines. A wheat line derived from a Uruguay landrace was shown to contain two resistance genes, one of which is likely a new wheat leaf rust resistance gene. The adult plant resistance in a line of winter wheat developed at Purdue University is likely made up of two previously described leaf rust resistance genes.

A new assay was developed that is able to distinguish between the different members of the wheat stem rust pathogen Ug99 race group from Africa. Methods were developed for genotyping field samples of killed wheat stem rust pathogen, which enables rapid monitoring for this pathogen on a global scale. Pilot project was completed with samples from Africa and Central Asia. New molecular assays were developed from rapid identification of rust fungi that are common pathogens of corn, and native prairie grasses that are being developed for biofuel production.


4.Accomplishments
1. Genome of the wheat stem rust pathogen was sequenced. Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust is an obligate biotrophic fungus that requires living tissue to grow, which has hampered the molecular analysis of this important plant pathogen. ARS researchers at St. Paul, Minnesota, collaborating with researchers at Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, sequenced the genome of P. graminis f. sp. tritici. The wheat stem rust pathogen genome is one of the largest and most complex, of any fungus studied to date and contains over 17,000 predicted proteins. An international group of scientists compared the genomes of P. graminis and the poplar leaf rust fungus (Melampsora larici-populina) to identified features that are related to pathogenicity and obligate biotrophic life-style in these two rust fungi. This represents the first complete genome sequencing of any rust fungus and provides important resources for the scientific community working on fungal plant pathogens and host resistance in cereal crops. In addition, this data has been used to develop rapid diagnostic methods for detection of critical strains of the wheat stem rust fungus.

2. Three new wheat stem rust resistance genes. New virulent races (Ug99 race group) of the wheat stem rust pathogen, P. graminis f. sp. tritici, found in Northeast Africa pose a significant risk to wheat and barley production in the United States. ARS researchers at St. Paul, Minnesota, in collaboration with an international team of scientists, have identified three new wheat stem rust resistance genes effective against Ug99. One of these genes was genetically mapped in common bread wheat and then combined by genetic crossing with a second stem rust resistance gene that was previously shown to be effective against Ug99. This new wheat line provides breeders with two-linked effective resistance genes, a key step in developing elite wheat cultivars highly resistant to Ug99 for farmers in the Unites States.

3. New host for the stem rust pathogen was found. The stem rust fungus requires an alternate host to complete its life cycle, and removal of these hosts from areas growing cereal crops has been used as an effective means of limiting genetic variability in this pathogen. Two common plant species, Mahonia repens (Creeping Oregon-grape) and M. aquifolium (Oregon-grape), were previously considered to be resistant to the stem rust pathogen, P. graminis. ARS scientists at St. Paul, Minnesota isolated P. graminis from infected fruit demonstrating that these common ornamental plants are susceptible to the stem rust fungus including economically important wheat stem rust pathogen. Creeping Oregon-grape and Oregon-grape are native to western North America and widely cultivated as ornamentals. This discovery provides an important new key in understanding the biology and epidemiology of this important wheat pathogen. This information will be used by scientists to identify regions of the United States where the potential for development of new races of this pathogen occur and develop surveillance strategies.

4. Intercontinental migration patterns of the wheat leaf rust pathogen. The wheat leaf rust fungus (Puccinia triticina) occurs worldwide and is capable of long distance transport and migration between continents. Genetic characterization of P. triticina populations is critical to determine migration patterns and detect virulent types that threaten wheat cultivars grown in the United States. ARS researchers at St. Paul, Minnesota, characterized isolates of P. triticina from Turkey, United Kingdom, Czech Republic, Slovakia, Italy, Spain, and Hungary. Eight distinct genetic populations were found in this European collection, one of which has high similarity with collections from the Middle East, South America and North America, indicating recent migration among these different continental regions. This information will be used by scientists to develop better models for the migration patterns of the wheat leaf rust pathogen.


Review Publications
Carson, M.L. 2010. Additional sources of broad-spectrum resistance to Puccinia coronata f. sp. avenae in Canadian accessions of Avena barbata. Plant Disease. 94:1405-1410.

Zhang, W., Olson, E., Saintenac, C., Rouse, M., Abate, Z., Jin, Y., Akhunov, E., Pumphrey, M., Dubcovsky, J. 2010. Genetic maps of stem rust resistance gene Sr35 in diploid and hexaploid wheat. Crop Science. 50(6):2464-2474.

Njau, P.N., Jin, Y., Huerta-Espino, J., Keller, B., Singh, R. 2010. Identification and evaluation of new sources of resistance to stem rust race Ug99 in wheat. Plant Disease. 94:413-419.

Crouch, J., Szabo, L.J. 2011. Real-time PCR discrimination of the southern and common corn rust pathogens Puccinia polysora and P. sorghi. Plant Disease. 95(6):624-632.

Duplessis, S., Cuomo, C.A., Lin, Y., Aerts, A., Tisserant, E., Veneault-Fourrey, C., Joly, D., Hacquard, S., Amselem, J., Cantarel, B., Chiu, R., Couthinho, P., Feau, N., Field, M., Frey, P., Gelhaye, E., Goldberg, J., Grabherr, M., Kodira, C., Kohler, A., Kues, U., Lindquist, E., Lucas, S., Mauceli, E., Morin, E., Murat, C., Pearson, M., Quesneville, H., Rouhier, N., Sakthikumar, S., Schmutz, J., Selles, B., Shapiro, H., Tangay, P., Tuskan, G.A., Van De Peer, Y., Henrissat, B., Rouze, P., Schein, J., Dodds, P.N., Zhong, S., Hamelin, R.C., Birren, B.W., Grigoriev, I.V., Szabo, L.J., Martin, F. 2011. Obligate biotrophy features unraveled by the genomic analysis of the rust fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici. Phytopathology. 108:9166-9171.

Kolmer, J.A., Anderson, J.A. 2011. First detection in North America of virulence in Puccinia triticina to wheat seedlings with Lr21. Plant Disease. 95:1032.

Kolmer, J.A., Anderson, J.A., Flor, J.M. 2010. Chromosome Location, Linkage with Simple Sequence Repeat Markers, and Leaf Rust Resistance Conditioned by Gene Lr63 in Wheat. Crop Science. 50:2392–2395.

Kolmer, J.A., Garvin, D.F., Jin, Y. 2011. Expression of a Thatcher wheat adult plant stem rust resistance QTL on chromosome arm 2BL is enhanced by Lr34. Crop Science. 51(2):526-533.

Kolmer, J.A., Long, D.L., Hughes, M.E. 2011. Physiologic specialization of Puccinia triticina on wheat in the United States in 2009. Plant Disease. 95:935-940.

Kolmer, J.A., Ordonez, M.E., Manisterski, J., Anikster, Y. 2011. Genetic differentiation of Puccinia triticina populations in the Middle East and genetic similarity with populations in Central Asia. Phytopathology. 101:870-877.

Niu, Z., Klindworth, D.L., Friesen, T.L., Chao, S., Jin, Y., Cai, X., Xu, S.S. 2011. Targeted introgression of a wheat stem rust resistance gene by DNA marker-assisted chromosome engineering genetics. Genetics. 187(4):1011-1021.

Qi, L.L., Pumphrey, M.O., Friebe, B., Zhang, P., Qian, C., Bowden, R.L., Rouse, M.N., Jin, Y., Gill, B.S. 2011. A novel Robertsonian translocation event leads to transfer of a stem rust resistance gene (Sr52) effective against race Ug99 from Dasypyrum villosum into bread wheat. Theoretical and Applied Genetics. 123:159-167.

Simons, K.J., Abate, Z., Chao, S., Zhang, W., Rouse, M., Jin, Y., Elias, E., Dubcovsky, J. 2011. Genetic mapping of stem rust resistance gene Sr13 in tetraploid wheat (Triticum turgidum subsp. durum L.). Theoretical and Applied Genetics. 122:649-658.

Tsilo, T., Jin, Y., Anderson, A. 2010. Identification of flanking markers for the stem rust resistance gene Sr6 in wheat. Crop Science. 50:1967-1970.

Liu, S., Yu, L., Singh, R., Jin, Y., Anderson, A. 2009. Diagnostic and co-dominant PCR markers for stem rust resistance genes Sr25 and Sr26. Theoretical and Applied Genetics. 120:691-697.

Ayliffe, M., Jin, Y., Kang, Z., Presson, M., Steffenson, B., Wang, S., Heung, H. 2011. Determining the basis of nonhost resistance in rice to cereal rusts. Euphytica. 179:33-40.

Glover, K.D., Rudd, J.C., Devkota, R.N., Hall, R.G., Jin, Y., Osborne, L.E., Ingemansen, J.A., Rickertsen, J.R., Hareland, G.A. 2011. Registration of "Select" Wheat. Journal of Plant Registrations. 5:196-201.

Jin, Y. 2011. Role of Berberis spp. as alternate hosts in generating new races of Puccinia graminis and P. striiformis. Euphytica. 179:105-108.

Liu, W., Pumphrey, M., Jin, Y., Rouse, M.N., Friebe, B., Gill, B. 2011. Development and characterization of wheat-Ae. searsii Robertsonian translocations and a recombinant chromosome conferring resistance to stem rust. Theoretical and Applied Genetics. 122:1537-1545.

Liu, W., Rouse, M.N., Friebe, B., Jin, Y., Gill, B., Pumphrey, M. 2011. Discovery and molecular mapping of a new gene conferring resistance to stem rust, Sr53, derived from Aegilops geniculata and characterization of spontaneous translocation stocks with reduced alien chromatin. Chromosome Research. 19(5):669-682.

Park, R.F., Fetch, T., Hodson, D., Jin, Y., Nazari, K., Pretorius, Z. 2011. International surveillance of wheat rust pathogens: progress and challenges. Euphytica. 179:109-117.

Rouse, M., Jin, Y. 2011. Stem rust resistance in A-genome diploid relatives of wheat. Plant Disease. 95:941-944.

Rouse, M.N., Wanyera, R., Njau, P., Jin, Y. 2011. Sources of resistance to stem rust race Ug99 in spring wheat germplasm. Plant Disease. 95:762-766.

Singh, R., Huerta-Espino, J., Bhavani, S., Herreta-Foessel, S., Singh, D., Singh, P., Velu, G., Mason, R., Jin, Y., Njau, P., Crossa, J. 2011. Race-nonspecific resistance to rust diseases in CIMMYT spring wheats (2010). Euphytica. 179:175-186.

Oliver, R.E., Lazo, G.R., Lutz, J.D., Rubenfield, M.J., Tinker, N.A., Anderson, J.M., Wisniewski-Morehead, N.H., Adhikary, D., Jellen, E.N., Maughan, P.J., Brown Guedira, G.L., Chao, S., Beattie, A.D., Carson, M.L., Rines, H.W., Obert, D.E., Bonman, J.M., Jackson, E.W. 2011. Model SNP development based on the complex oat genome using high-throughput 454 sequencing technology. Biomed Central (BMC) Genomics. 12:77.

Last Modified: 9/1/2014
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